X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=7e37277b2926bd797f0ebd343f5fc3d9df4c2fd8;hb=4cdc5b801cd2a0f2786ab753900e4ce774099ad8;hp=4fc88141cff64812809c1c38911fb422a269d79a;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 4fc8814..7e37277 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -20,14 +20,20 @@
  */
 package MCview;
 
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-
 import jalview.analysis.AlignSeq;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
 
 public class PDBfile extends jalview.io.AlignFile
 {
@@ -40,14 +46,33 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws IOException
+  boolean processSecondaryStructure=true;
+  
+
+  public PDBfile(boolean visibleChainAnnotation,
+          boolean processSecondaryStructure)
   {
-    super(inFile, inType);
+    super();
+    VisibleChainAnnotation = visibleChainAnnotation;
+    this.processSecondaryStructure = processSecondaryStructure;
   }
 
-  public PDBfile(FileParse source) throws IOException
+  public PDBfile(boolean visibleChainAnnotation,
+          boolean processSecondaryStructure, String file, String protocol) throws IOException
   {
-    super(source);
+    super(false, file, protocol);
+    VisibleChainAnnotation = visibleChainAnnotation;
+    this.processSecondaryStructure = processSecondaryStructure;
+    doParse();
+  }
+
+  public PDBfile(boolean visibleChainAnnotation,
+          boolean processSecondaryStructure, FileParse source) throws IOException
+  {
+    super(false, source);
+    VisibleChainAnnotation = visibleChainAnnotation;
+    this.processSecondaryStructure = processSecondaryStructure;
+    doParse();
   }
 
   public String print()
@@ -61,7 +86,7 @@ public class PDBfile extends jalview.io.AlignFile
     id = safeName(getDataName());
 
     chains = new Vector();
-    ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
+    ArrayList<SequenceI> rna = new ArrayList<SequenceI>(), prot = new ArrayList<SequenceI>();
     PDBChain tmpchain;
     String line = null;
     boolean modelFlag = false;
@@ -161,8 +186,10 @@ public class PDBfile extends jalview.io.AlignFile
         PDBEntry entry = new PDBEntry();
         entry.setId(id);
         entry.setProperty(new Hashtable());
-        if (((PDBChain)chains.elementAt(i)).id!=null) {
-          entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+        if (((PDBChain) chains.elementAt(i)).id != null)
+        {
+          entry.getProperty().put("CHAIN",
+                  ((PDBChain) chains.elementAt(i)).id);
         }
         if (inFile != null)
         {
@@ -178,56 +205,62 @@ public class PDBfile extends jalview.io.AlignFile
         // maintain reference to
         // dataset
         seqs.addElement(chainseq);
-       if(isRNA(chainseq)==true)
-       {
-         rna.add(chainseq);
-       } else {
-         prot.add(chainseq);
-       }
-         
+        if (isRNA(chainseq) == true)
+        {
+          rna.add(chainseq);
+        }
+        else
+        {
+          prot.add(chainseq);
+        }
+
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-        
+
         if (chainannot != null)
         {
           for (int ai = 0; ai < chainannot.length; ai++)
           {
-        
             chainannot[ai].visible = VisibleChainAnnotation;
             annotations.addElement(chainannot[ai]);
           }
         }
       }
-      if (rna.size()>0)
-      try {
-        processPdbFileWithAnnotate3d(rna);
-      } catch (Exception x)
+      if (processSecondaryStructure)
       {
-        System.err.println("Exceptions when dealing with RNA in pdb file");
-        x.printStackTrace();
-        
-      };
-      if (prot.size()>0)
-      try {
-        processPdbFileWithJmol(prot);
-      } catch (Exception x)
+      if (rna.size() > 0)
       {
-        System.err.println("Exceptions when dealing with RNA in pdb file");
-        x.printStackTrace();
-        
-      };
-      if (prot.size()>0)
-      try {
-        processPdbFileWithJmol(prot);
-      } catch (Exception x)
+        try
+        {
+          processPdbFileWithAnnotate3d(rna);
+        } catch (Exception x)
+        {
+          System.err
+                  .println("Exceptions when dealing with RNA in pdb file");
+          x.printStackTrace();
+
+        }
+      }
+      ;
+      if (prot.size() > 0)
       {
-        System.err.println("Exceptions when dealing with RNA in pdb file");
-        x.printStackTrace();
-        
-      };
+        try
+        {
+          processPdbFileWithJmol(prot);
+        } catch (Exception x)
+        {
+          System.err
+                  .println("Exceptions from Jmol when processing data in pdb file");
+          x.printStackTrace();
+
+        }
+      }
+      }
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
-      throw new IOException("Out of memory loading PDB File");
+      throw new IOException(
+              MessageManager
+                      .getString("exception.outofmemory_loading_pdb_file"));
     } catch (NumberFormatException ex)
     {
       if (line != null)
@@ -236,95 +269,82 @@ public class PDBfile extends jalview.io.AlignFile
         System.err.println(line);
       }
     }
+    markCalcIds();
+  }
+
+  public static boolean isCalcIdForFile(String calcId, String pdbFile)
+  {
+    return (calcId != null && calcId.startsWith("JalviewPDB:" + pdbFile
+            + ":JalviewPDB:"));
+  }
+  private void markCalcIds()
+  {
+    for (SequenceI sq : seqs)
+    {
+      for (AlignmentAnnotation aa : sq.getAnnotation())
+      {
+        String oldId = aa.getCalcId();
+        if (oldId == null)
+        {
+          oldId = "";
+        }
+        aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
+      }
+    }
   }
-  private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
+  private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
+          throws Exception
   {
-    try {
+    try
+    {
       Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
-      if (cl!=null)
+      if (cl != null)
       {
-        Object jmf = cl.getConstructor(new Class[] {FileParse.class}).newInstance(new Object[] {new FileParse(getDataName(),type)});
-        Alignment al = new Alignment((SequenceI[]) cl.getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
-        cl.getMethod("addAnnotations",new Class[] {Alignment.class}).invoke(jmf, al);
-        replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+        Object jmf = cl.getConstructor(new Class[]
+        { FileParse.class }).newInstance(new Object[]
+        { new FileParse(getDataName(), type) });
+        Alignment al = new Alignment((SequenceI[]) cl.getMethod(
+                "getSeqsAsArray", new Class[]
+                {}).invoke(jmf));
+        cl.getMethod("addAnnotations", new Class[]
+        { Alignment.class }).invoke(jmf, al);
+        AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
       }
     } catch (ClassNotFoundException q)
-    {}
-  }
-  private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
-//    System.out.println("this is a PDB format and RNA sequence");
-    // note: we use reflection here so that the applet can compile and run without the HTTPClient bits and pieces needed for accessing Annotate3D web service
-    try {
-    Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
-    if (cl!=null)
     {
-      // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service
-      Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(new Object[] {});
-      AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", new Class[] { FileParse.class}).invoke(annotate3d, new Object[] { new FileParse(getDataName(),type)}));
-      replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
     }
-    } catch (ClassNotFoundException x)
-    {
-      //ignore classnotfounds - occurs in applet
-    };
   }
-  private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
+
+  private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna)
+          throws Exception
   {
-    if (al!=null && al.getHeight()>0)
+    // System.out.println("this is a PDB format and RNA sequence");
+    // note: we use reflection here so that the applet can compile and run
+    // without the HTTPClient bits and pieces needed for accessing Annotate3D
+    // web service
+    try
     {
-      ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
-      ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
-      
-      for (SequenceI sq:ochains)
+      Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+      if (cl != null)
       {
-        SequenceI bestm=null;
-        AlignSeq bestaseq=null;
-        int bestscore=0;
-        for (SequenceI msq:al.getSequences())
-        {
-          AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
-          if (bestm==null || aseq.getMaxScore()>bestscore)
-          {
-            bestscore=aseq.getMaxScore();
-            bestaseq= aseq;
-            bestm=msq;
-          }
-        }
-        System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
-        matches.add(bestm);
-        aligns.add(bestaseq);
-        al.deleteSequence(bestm);
-      }
-      for (int p=0,pSize=seqs.size();p<pSize;p++)
-      {
-        SequenceI sq,sp=seqs.get(p);
-        int q;
-        if ((q=ochains.indexOf(sp))>-1)
-        {
-          seqs.set(p, sq=matches.get(q));
-          sq.setName(sp.getName());
-          sq.setDescription(sp.getDescription());
-          sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
-          int inspos=-1;
-          for (int ap=0;ap<annotations.size();)
-          {
-            if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
-              if (inspos==-1)
-              {
-                inspos=ap;
-              }
-              annotations.remove(ap);
-            } else {
-              ap++;
-            }
-          }
-          if (sq.getAnnotation()!=null) {
-            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
-          }
-        }
+        // TODO: use the PDB ID of the structure if one is available, to save
+        // bandwidth and avoid uploading the whole structure to the service
+        Object annotate3d = cl.getConstructor(new Class[]
+        {}).newInstance(new Object[]
+        {});
+        AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
+                new Class[]
+                { FileParse.class }).invoke(annotate3d, new Object[]
+        { new FileParse(getDataName(), type) }));
+        AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
       }
+    } catch (ClassNotFoundException x)
+    {
+      // ignore classnotfounds - occurs in applet
     }
+    ;
   }
+
   /**
    * make a friendly ID string.
    * 
@@ -391,20 +411,22 @@ public class PDBfile extends jalview.io.AlignFile
     for (int i = 0; i < chains.size(); i++)
     {
       ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
-              1.0f / (float) i, .4f, 1.0f));
+              1.0f / i, .4f, 1.0f));
     }
   }
+
   public boolean isRNA(SequenceI seqs)
   {
-	  for (int i=0;i<seqs.getLength();i++){
-		  if((seqs.getCharAt(i)!='A') &&(seqs.getCharAt(i)!='C')&&(seqs.getCharAt(i)!='G')&&(seqs.getCharAt(i)!='U'))
-		  {
-			  return false;
-		  }
-	  }
-	 
-		  return true;
-	  
-	  
+    for (int i = 0; i < seqs.getLength(); i++)
+    {
+      if ((seqs.getCharAt(i) != 'A') && (seqs.getCharAt(i) != 'C')
+              && (seqs.getCharAt(i) != 'G') && (seqs.getCharAt(i) != 'U'))
+      {
+        return false;
+      }
+    }
+
+    return true;
+
   }
 }